Question: In Cell Ranger v9.0, the barcode inclusion list names for 3' assays have been updated to include suffixes like _TRU and _NXT. What is the reason for this change, and why were the names renamed?
Answer:
Starting from Cell Ranger v9.0, the 3'v3 and 3'v4 barcode inclusion lists have been renamed to distinguish between different capture strategies used for Feature Barcode libraries.
The 3'GEM-X inclusion list 3M-3pgex-may-2023.txt.gz was renamed to 3M-3pgex-may-2023_TRU.txt.gz, and the 3' NextGEM inclusion list, 3M-febrary-2018.txt.gz was renamed to 3M-febrary-2018_TRU.txt.gz.
- For Poly-A capture, the v9 pipeline will use the inclusion list,
3M-3pgex-may-2023_TRU.txt.gzor3M-febrary-2018_TRU.txt.gz. - For Capture Sequence 1, the v9 pipeline will use the barcode inclusion list file,
3M-3pgex-may-2023_NXT.txt.gzand 3M-february-2018_NXT.txt.gz, located atcellranger-x.y.z/lib/python/cellranger/barcodes/translation. For more details on feature barcode translations, please see this article here.
Products: Chromium Universal 3' Single Cell
Last Updated: Feb 2025